[BioC] extract data from RangedData table (IRange TEQC packages)

nathalie nac at sanger.ac.uk
Thu Apr 19 17:29:24 CEST 2012


Hi,
I would like to extract a txt file of a RangedData table I have created 
with TEQC package using the get.targets function and a bed target file 
"file" as an input:

 > targets<-get.targets("file", chrcol=1,startcol=2,endcol=3, 
zerobased=F, sep="\t",skip=0)

[1] "read 1243 target regions in total, which are collapsed to 598 
non-overlapping target regions"

 > targets
RangedData with 598 rows and 0 value columns across 18 spaces
        space                 ranges   |
<factor> <IRanges>   |
1       Chr1 [115247090, 115250671]   |
2       Chr1 [115250775, 115250813]   |
3       Chr1 [115251152, 115251275]   |
4       Chr1 [115252190, 115252349]   |
5       Chr1 [115256421, 115256599]   |
6       Chr1 [115258671, 115258798]   |
7       Chr1 [115259279, 115259515]   |
8      Chr10 [ 89622870,  89624305]   |
9      Chr10 [ 89626430,  89626806]   |
...      ...                    ... ...
590     ChrX [133607389, 133607495]   |
591     ChrX [133609211, 133609394]   |
592     ChrX [133620495, 133620560]   |
593     ChrX [133620692, 133620696]   |
594     ChrX [133624218, 133624235]   |
595     ChrX [133627538, 133627620]   |
596     ChrX [133632420, 133632466]   |
597     ChrX [133632638, 133632714]   |
598     ChrX [133634060, 133634698]   |


I would like to extract the collapsed chromosome start and end points 
from this to a txt file? Any suggestions would be welcome...

output file should contain:
Chr1 115247090, 115250671
Chr1 115250775, 115250813
Chr1 115251152, 115251275
.....


Many thanks,
Nat


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